Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016409.1 Corchorus olitorius cultivar O-4 contig16442, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 5930
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34


Found at i:1612 original size:30 final size:31

Alignment explanation


    Indices: 1571--1641  Score: 83
    Period size: 30  Copynumber: 2.4  Consensus size: 31

       1561 ACACCTCAAA

                *       *                  
       1571 CAAGCCTCAAATTGCAGAAATCAAGT-ATAT
          1 CAAGTCTCAAATAGCAGAAATCAAGTAATAT

                            **    *        
       1601 CAAGTCTCAAATAGCATCAATCCAGTAATAT
          1 CAAGTCTCAAATAGCAGAAATCAAGTAATAT

                       
       1632 C-AGTCTCAAA
          1 CAAGTCTCAAA

       1642 CTTATAAAAA


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  30   30  0.86
  31    5  0.14

ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24


Consensus pattern (31 bp):   
CAAGTCTCAAATAGCAGAAATCAAGTAATAT

Found at i:4513 original size:29 final size:29

Alignment explanation


    Indices: 4465--4583  Score: 204
    Period size: 29  Copynumber: 4.1  Consensus size: 29

       4455 AAAACACCTA

                                     *   
       4465 GATGTGC-AAAATGACCAAAATGCCCCTG
          1 GATGTGCAAAAATGACCAAAATGCCACTG

                      *              *   
       4493 GATGTGCAAATATGACCAAAATGCCCCTG
          1 GATGTGCAAAAATGACCAAAATGCCACTG

                                         
       4522 GATGTGCAAAAATGACCAAAATGCCACTG
          1 GATGTGCAAAAATGACCAAAATGCCACTG

                                         
       4551 GATGTGCAAAAATGACCAAAATGCCACTG
          1 GATGTGCAAAAATGACCAAAATGCCACTG

                
       4580 GATG
          1 GATG

       4584 AGCGACCCTA


Statistics
Matches: 87,  Mismatches: 3, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  28    7  0.08
  29   80  0.92

ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18


Consensus pattern (29 bp):   
GATGTGCAAAAATGACCAAAATGCCACTG

Found at i:4880 original size:35 final size:35

Alignment explanation


    Indices: 4839--5043  Score: 347
    Period size: 35  Copynumber: 5.9  Consensus size: 35

       4829 TGAGTTCATA

                          *            *       
       4839 TTGAAGATGCTACATCGAGTCATCTGACTTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                         *     
       4874 TTGAAGATGCTACACCGAGTCATCTGAATCTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                       *                       
       4909 TTGAAGATGCTGCACCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                         *     
       4944 TTGAAGATGCTACACCGAGTCATCTGAATCTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                       *  *                    
       4979 TTGAAGATGCTGCATCGAGTCATCTGAATTTGTCT
          1 TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

                                          
       5014 TTGAAGATGCTACACCGAGTCATCTGAATT
          1 TTGAAGATGCTACACCGAGTCATCTGAATT

       5044 CCTGAGAATT


Statistics
Matches: 158,  Mismatches: 12, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  35  158  1.00

ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34


Consensus pattern (35 bp):   
TTGAAGATGCTACACCGAGTCATCTGAATTTGTCT

Found at i:5533 original size:2 final size:2

Alignment explanation


    Indices: 5526--5551  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       5516 ATAAACTTAG

                                                  
       5526 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       5552 TAACAAAAGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.